Starting phenix.real_space_refine on Wed Jul 30 05:58:41 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9f10_50120/07_2025/9f10_50120.cif Found real_map, /net/cci-nas-00/data/ceres_data/9f10_50120/07_2025/9f10_50120.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.94 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9f10_50120/07_2025/9f10_50120.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9f10_50120/07_2025/9f10_50120.map" model { file = "/net/cci-nas-00/data/ceres_data/9f10_50120/07_2025/9f10_50120.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9f10_50120/07_2025/9f10_50120.cif" } resolution = 2.94 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.001 sd= 0.056 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 6 Type Number sf(0) Gaussians P 181 5.49 5 Mg 1 5.21 5 S 35 5.16 5 C 7123 2.51 5 N 2238 2.21 5 O 2708 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 6 residue(s): 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5711/modules/chem_data/mon_lib" Total number of atoms: 12286 Number of models: 1 Model: "" Number of chains: 9 Chain: "A" Number of atoms: 1982 Number of conformers: 1 Conformer: "" Number of residues, atoms: 96, 1982 Classifications: {'DNA': 96} Link IDs: {'rna3p': 95} Chain: "B" Number of atoms: 1739 Number of conformers: 1 Conformer: "" Number of residues, atoms: 85, 1739 Classifications: {'DNA': 85} Link IDs: {'rna3p': 84} Chain: "C" Number of atoms: 764 Number of conformers: 1 Conformer: "" Number of residues, atoms: 95, 764 Classifications: {'peptide': 95} Link IDs: {'PTRANS': 5, 'TRANS': 89} Chain: "D" Number of atoms: 749 Number of conformers: 1 Conformer: "" Number of residues, atoms: 94, 749 Classifications: {'peptide': 94} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 5, 'TRANS': 88} Chain: "E" Number of atoms: 906 Number of conformers: 1 Conformer: "" Number of residues, atoms: 112, 906 Classifications: {'peptide': 112} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 3, 'TRANS': 108} Chain breaks: 1 Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 2 Planarities with less than four sites: {'ASN:plan1': 1} Unresolved non-hydrogen planarities: 3 Chain: "F" Number of atoms: 972 Number of conformers: 1 Conformer: "" Number of residues, atoms: 120, 972 Classifications: {'peptide': 120} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 3, 'TRANS': 116} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 4 Chain: "G" Number of atoms: 867 Number of conformers: 1 Conformer: "" Number of residues, atoms: 109, 867 Classifications: {'peptide': 109} Incomplete info: {'truncation_to_alanine': 7} Link IDs: {'PTRANS': 3, 'TRANS': 105} Unresolved non-hydrogen bonds: 26 Unresolved non-hydrogen angles: 32 Unresolved non-hydrogen dihedrals: 23 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'TYR:plan': 1, 'ASN:plan1': 1} Unresolved non-hydrogen planarities: 10 Chain: "H" Number of atoms: 4306 Number of conformers: 1 Conformer: "" Number of residues, atoms: 564, 4306 Classifications: {'peptide': 564} Incomplete info: {'truncation_to_alanine': 13} Link IDs: {'PTRANS': 22, 'TRANS': 541} Chain breaks: 3 Unresolved non-hydrogen bonds: 47 Unresolved non-hydrogen angles: 60 Unresolved non-hydrogen dihedrals: 36 Unresolved non-hydrogen chiralities: 4 Planarities with less than four sites: {'GLN:plan1': 1, 'ARG:plan': 2, 'HIS:plan': 1, 'ASN:plan1': 1, 'ASP:plan': 3} Unresolved non-hydrogen planarities: 31 Chain: "H" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' MG': 1} Classifications: {'undetermined': 1} Time building chain proxies: 11.22, per 1000 atoms: 0.91 Number of scatterers: 12286 At special positions: 0 Unit cell: (93.225, 131.175, 182.325, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) S 35 16.00 P 181 15.00 Mg 1 11.99 O 2708 8.00 N 2238 7.00 C 7123 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 2.78 Conformation dependent library (CDL) restraints added in 1.2 seconds 2148 Ramachandran restraints generated. 1074 Oldfield, 0 Emsley, 1074 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2038 Finding SS restraints... Secondary structure from input PDB file: 39 helices and 14 sheets defined 46.1% alpha, 17.1% beta 71 base pairs and 160 stacking pairs defined. Time for finding SS restraints: 4.80 Creating SS restraints... Processing helix chain 'C' and resid 4 through 17 Processing helix chain 'C' and resid 19 through 40 removed outlier: 3.577A pdb=" N PHE C 31 " --> pdb=" O VAL C 27 " (cutoff:3.500A) removed outlier: 3.610A pdb=" N ILE C 34 " --> pdb=" O PHE C 30 " (cutoff:3.500A) Processing helix chain 'C' and resid 84 through 92 Processing helix chain 'D' and resid 2 through 14 Processing helix chain 'D' and resid 18 through 39 Processing helix chain 'D' and resid 83 through 91 Processing helix chain 'E' and resid 20 through 34 Processing helix chain 'E' and resid 36 through 52 Processing helix chain 'E' and resid 75 through 90 Processing helix chain 'E' and resid 92 through 108 Processing helix chain 'F' and resid 20 through 34 removed outlier: 4.138A pdb=" N SER F 24 " --> pdb=" O VAL F 20 " (cutoff:3.500A) removed outlier: 4.557A pdb=" N LEU F 25 " --> pdb=" O ASP F 21 " (cutoff:3.500A) removed outlier: 3.656A pdb=" N LEU F 26 " --> pdb=" O VAL F 22 " (cutoff:3.500A) Processing helix chain 'F' and resid 36 through 52 Processing helix chain 'F' and resid 75 through 90 Processing helix chain 'F' and resid 92 through 108 Processing helix chain 'G' and resid 20 through 34 removed outlier: 4.067A pdb=" N SER G 24 " --> pdb=" O VAL G 20 " (cutoff:3.500A) removed outlier: 4.283A pdb=" N LEU G 25 " --> pdb=" O ASP G 21 " (cutoff:3.500A) Processing helix chain 'G' and resid 36 through 52 removed outlier: 3.801A pdb=" N HIS G 50 " --> pdb=" O LYS G 46 " (cutoff:3.500A) Processing helix chain 'G' and resid 75 through 90 Processing helix chain 'G' and resid 92 through 108 Processing helix chain 'H' and resid 9 through 18 removed outlier: 3.598A pdb=" N THR H 18 " --> pdb=" O GLY H 14 " (cutoff:3.500A) Processing helix chain 'H' and resid 35 through 41 Processing helix chain 'H' and resid 48 through 58 Processing helix chain 'H' and resid 87 through 98 Processing helix chain 'H' and resid 99 through 101 No H-bonds generated for 'chain 'H' and resid 99 through 101' Processing helix chain 'H' and resid 102 through 118 Processing helix chain 'H' and resid 184 through 192 Processing helix chain 'H' and resid 192 through 210 Processing helix chain 'H' and resid 219 through 222 removed outlier: 3.618A pdb=" N GLY H 222 " --> pdb=" O GLY H 219 " (cutoff:3.500A) No H-bonds generated for 'chain 'H' and resid 219 through 222' Processing helix chain 'H' and resid 231 through 234 Processing helix chain 'H' and resid 235 through 246 Processing helix chain 'H' and resid 250 through 262 Processing helix chain 'H' and resid 269 through 285 removed outlier: 3.669A pdb=" N LYS H 273 " --> pdb=" O ASP H 269 " (cutoff:3.500A) Processing helix chain 'H' and resid 294 through 302 removed outlier: 3.609A pdb=" N ARG H 298 " --> pdb=" O ALA H 294 " (cutoff:3.500A) removed outlier: 3.540A pdb=" N ASP H 300 " --> pdb=" O ASP H 296 " (cutoff:3.500A) removed outlier: 4.105A pdb=" N LEU H 301 " --> pdb=" O GLN H 297 " (cutoff:3.500A) Processing helix chain 'H' and resid 576 through 594 Processing helix chain 'H' and resid 603 through 622 Processing helix chain 'H' and resid 642 through 650 removed outlier: 3.815A pdb=" N TYR H 645 " --> pdb=" O ARG H 642 " (cutoff:3.500A) removed outlier: 6.223A pdb=" N ARG H 647 " --> pdb=" O ARG H 644 " (cutoff:3.500A) removed outlier: 6.659A pdb=" N ASP H 648 " --> pdb=" O TYR H 645 " (cutoff:3.500A) removed outlier: 3.507A pdb=" N MET H 649 " --> pdb=" O LEU H 646 " (cutoff:3.500A) Processing helix chain 'H' and resid 696 through 698 No H-bonds generated for 'chain 'H' and resid 696 through 698' Processing helix chain 'H' and resid 793 through 797 removed outlier: 4.033A pdb=" N MET H 797 " --> pdb=" O GLN H 794 " (cutoff:3.500A) Processing helix chain 'H' and resid 798 through 808 removed outlier: 3.509A pdb=" N SER H 808 " --> pdb=" O GLY H 804 " (cutoff:3.500A) Processing helix chain 'H' and resid 822 through 827 removed outlier: 3.771A pdb=" N LYS H 826 " --> pdb=" O ARG H 822 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'C' and resid 44 through 46 Processing sheet with id=AA2, first strand: chain 'C' and resid 60 through 63 Processing sheet with id=AA3, first strand: chain 'D' and resid 43 through 45 Processing sheet with id=AA4, first strand: chain 'D' and resid 59 through 62 Processing sheet with id=AA5, first strand: chain 'E' and resid 13 through 19 Processing sheet with id=AA6, first strand: chain 'F' and resid 13 through 19 Processing sheet with id=AA7, first strand: chain 'G' and resid 16 through 19 Processing sheet with id=AA8, first strand: chain 'H' and resid 2 through 7 removed outlier: 4.347A pdb=" N GLY H 79 " --> pdb=" O VAL H 7 " (cutoff:3.500A) removed outlier: 5.584A pdb=" N GLN H 155 " --> pdb=" O THR H 148 " (cutoff:3.500A) removed outlier: 4.733A pdb=" N VAL H 140 " --> pdb=" O ALA H 163 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'H' and resid 69 through 70 Processing sheet with id=AB1, first strand: chain 'H' and resid 122 through 123 Processing sheet with id=AB2, first strand: chain 'H' and resid 216 through 217 Processing sheet with id=AB3, first strand: chain 'H' and resid 568 through 572 removed outlier: 6.678A pdb=" N VAL H 788 " --> pdb=" O ARG H 813 " (cutoff:3.500A) removed outlier: 7.013A pdb=" N TYR H 815 " --> pdb=" O VAL H 788 " (cutoff:3.500A) removed outlier: 6.699A pdb=" N ALA H 790 " --> pdb=" O TYR H 815 " (cutoff:3.500A) removed outlier: 6.726A pdb=" N VAL H 598 " --> pdb=" O PHE H 789 " (cutoff:3.500A) removed outlier: 7.914A pdb=" N SER H 791 " --> pdb=" O VAL H 598 " (cutoff:3.500A) removed outlier: 7.031A pdb=" N GLN H 600 " --> pdb=" O SER H 791 " (cutoff:3.500A) removed outlier: 9.073A pdb=" N GLU H 776 " --> pdb=" O SER H 597 " (cutoff:3.500A) removed outlier: 6.379A pdb=" N ALA H 599 " --> pdb=" O GLU H 776 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'H' and resid 628 through 636 removed outlier: 6.501A pdb=" N THR H 682 " --> pdb=" O ASP H 672 " (cutoff:3.500A) removed outlier: 4.682A pdb=" N VAL H 674 " --> pdb=" O SER H 680 " (cutoff:3.500A) removed outlier: 6.821A pdb=" N SER H 680 " --> pdb=" O VAL H 674 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'H' and resid 756 through 759 removed outlier: 6.403A pdb=" N VAL H 748 " --> pdb=" O VAL H 737 " (cutoff:3.500A) removed outlier: 5.972A pdb=" N VAL H 737 " --> pdb=" O VAL H 748 " (cutoff:3.500A) 447 hydrogen bonds defined for protein. 1287 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 161 hydrogen bonds 318 hydrogen bond angles 0 basepair planarities 71 basepair parallelities 160 stacking parallelities Total time for adding SS restraints: 5.33 Time building geometry restraints manager: 3.37 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 2661 1.33 - 1.45: 3493 1.45 - 1.57: 6299 1.57 - 1.69: 360 1.69 - 1.81: 67 Bond restraints: 12880 Sorted by residual: bond pdb=" CA ILE C 71 " pdb=" C ILE C 71 " ideal model delta sigma weight residual 1.524 1.505 0.019 8.30e-03 1.45e+04 5.24e+00 bond pdb=" CA ILE H 724 " pdb=" C ILE H 724 " ideal model delta sigma weight residual 1.526 1.510 0.016 7.90e-03 1.60e+04 4.31e+00 bond pdb=" P DG A 9 " pdb=" OP2 DG A 9 " ideal model delta sigma weight residual 1.480 1.516 -0.036 2.00e-02 2.50e+03 3.24e+00 bond pdb=" P DG A 9 " pdb=" OP1 DG A 9 " ideal model delta sigma weight residual 1.480 1.515 -0.035 2.00e-02 2.50e+03 3.08e+00 bond pdb=" P DT B 82 " pdb=" OP1 DT B 82 " ideal model delta sigma weight residual 1.480 1.515 -0.035 2.00e-02 2.50e+03 3.06e+00 ... (remaining 12875 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.55: 17479 1.55 - 3.11: 611 3.11 - 4.66: 53 4.66 - 6.22: 16 6.22 - 7.77: 5 Bond angle restraints: 18164 Sorted by residual: angle pdb=" O3' DT A 64 " pdb=" P DA A 63 " pdb=" O5' DA A 63 " ideal model delta sigma weight residual 104.00 97.91 6.09 1.50e+00 4.44e-01 1.65e+01 angle pdb=" N LEU H 802 " pdb=" CA LEU H 802 " pdb=" C LEU H 802 " ideal model delta sigma weight residual 111.36 107.08 4.28 1.09e+00 8.42e-01 1.54e+01 angle pdb=" N GLY H 30 " pdb=" CA GLY H 30 " pdb=" C GLY H 30 " ideal model delta sigma weight residual 113.18 120.95 -7.77 2.37e+00 1.78e-01 1.08e+01 angle pdb=" O3' DA B 83 " pdb=" P DT B 84 " pdb=" O5' DT B 84 " ideal model delta sigma weight residual 104.00 99.59 4.41 1.50e+00 4.44e-01 8.64e+00 angle pdb=" C3' DT A 64 " pdb=" O3' DT A 64 " pdb=" P DA A 63 " ideal model delta sigma weight residual 120.20 124.54 -4.34 1.50e+00 4.44e-01 8.36e+00 ... (remaining 18159 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.83: 6604 35.83 - 71.66: 793 71.66 - 107.49: 5 107.49 - 143.32: 2 143.32 - 179.15: 5 Dihedral angle restraints: 7409 sinusoidal: 4261 harmonic: 3148 Sorted by residual: dihedral pdb=" CA VAL H 229 " pdb=" C VAL H 229 " pdb=" N PRO H 230 " pdb=" CA PRO H 230 " ideal model delta harmonic sigma weight residual -180.00 -154.16 -25.84 0 5.00e+00 4.00e-02 2.67e+01 dihedral pdb=" CA MET H 29 " pdb=" C MET H 29 " pdb=" N GLY H 30 " pdb=" CA GLY H 30 " ideal model delta harmonic sigma weight residual 180.00 157.01 22.99 0 5.00e+00 4.00e-02 2.11e+01 dihedral pdb=" CA PHE E 4 " pdb=" C PHE E 4 " pdb=" N GLY E 5 " pdb=" CA GLY E 5 " ideal model delta harmonic sigma weight residual 180.00 -158.69 -21.31 0 5.00e+00 4.00e-02 1.82e+01 ... (remaining 7406 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.113: 1989 0.113 - 0.227: 20 0.227 - 0.340: 0 0.340 - 0.454: 3 0.454 - 0.567: 4 Chirality restraints: 2016 Sorted by residual: chirality pdb=" P DG A 9 " pdb=" OP1 DG A 9 " pdb=" OP2 DG A 9 " pdb=" O5' DG A 9 " both_signs ideal model delta sigma weight residual True 2.35 -2.91 -0.57 2.00e-01 2.50e+01 8.03e+00 chirality pdb=" P DT B 82 " pdb=" OP1 DT B 82 " pdb=" OP2 DT B 82 " pdb=" O5' DT B 82 " both_signs ideal model delta sigma weight residual True 2.35 -2.84 -0.50 2.00e-01 2.50e+01 6.17e+00 chirality pdb=" P DT A 8 " pdb=" OP1 DT A 8 " pdb=" OP2 DT A 8 " pdb=" O5' DT A 8 " both_signs ideal model delta sigma weight residual True 2.35 -2.83 -0.49 2.00e-01 2.50e+01 5.89e+00 ... (remaining 2013 not shown) Planarity restraints: 1716 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ARG C 60 " -0.032 5.00e-02 4.00e+02 4.84e-02 3.74e+00 pdb=" N PRO C 61 " 0.084 5.00e-02 4.00e+02 pdb=" CA PRO C 61 " -0.025 5.00e-02 4.00e+02 pdb=" CD PRO C 61 " -0.027 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C LEU H 60 " -0.031 5.00e-02 4.00e+02 4.76e-02 3.63e+00 pdb=" N PRO H 61 " 0.082 5.00e-02 4.00e+02 pdb=" CA PRO H 61 " -0.024 5.00e-02 4.00e+02 pdb=" CD PRO H 61 " -0.026 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C1' DT A 60 " -0.024 2.00e-02 2.50e+03 1.14e-02 3.27e+00 pdb=" N1 DT A 60 " 0.023 2.00e-02 2.50e+03 pdb=" C2 DT A 60 " 0.002 2.00e-02 2.50e+03 pdb=" O2 DT A 60 " 0.003 2.00e-02 2.50e+03 pdb=" N3 DT A 60 " 0.001 2.00e-02 2.50e+03 pdb=" C4 DT A 60 " -0.001 2.00e-02 2.50e+03 pdb=" O4 DT A 60 " -0.012 2.00e-02 2.50e+03 pdb=" C5 DT A 60 " 0.003 2.00e-02 2.50e+03 pdb=" C7 DT A 60 " 0.001 2.00e-02 2.50e+03 pdb=" C6 DT A 60 " 0.005 2.00e-02 2.50e+03 ... (remaining 1713 not shown) Histogram of nonbonded interaction distances: 1.86 - 2.47: 43 2.47 - 3.07: 7888 3.07 - 3.68: 19407 3.68 - 4.29: 30240 4.29 - 4.90: 45459 Nonbonded interactions: 103037 Sorted by model distance: nonbonded pdb=" OP1 DG A -1 " pdb="MG MG H1801 " model vdw 1.857 2.170 nonbonded pdb=" O3' DT A 1 " pdb="MG MG H1801 " model vdw 1.997 2.170 nonbonded pdb=" NE2 HIS H 157 " pdb="MG MG H1801 " model vdw 2.047 2.250 nonbonded pdb=" OG SER H 122 " pdb=" OG SER H 176 " model vdw 2.101 3.040 nonbonded pdb=" OD1 ASP G 75 " pdb=" OG1 THR G 78 " model vdw 2.220 3.040 ... (remaining 103032 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = (chain 'E' and (resid 11 through 53 or (resid 54 and (name N or name CA or name \ C or name O or name CB )) or resid 55 through 60 or (resid 62 and (name N or nam \ e CA or name C or name O or name CB )) or resid 63 or (resid 64 through 66 and ( \ name N or name CA or name C or name O or name CB )) or resid 67 through 113)) selection = (chain 'F' and (resid 11 through 59 or (resid 60 and (name N or name CA or name \ C or name O or name CB )) or (resid 62 and (name N or name CA or name C or name \ O or name CB )) or resid 63 or (resid 64 through 66 and (name N or name CA or na \ me C or name O or name CB )) or resid 67 through 113)) selection = (chain 'G' and (resid 11 through 60 or resid 62 through 113)) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 10.480 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.490 Check model and map are aligned: 0.080 Set scattering table: 0.120 Process input model: 37.430 Find NCS groups from input model: 0.240 Set up NCS constraints: 0.050 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:15.130 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 64.040 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7836 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.045 12880 Z= 0.244 Angle : 0.645 7.771 18164 Z= 0.375 Chirality : 0.048 0.567 2016 Planarity : 0.004 0.048 1716 Dihedral : 22.948 179.153 5371 Min Nonbonded Distance : 1.857 Molprobity Statistics. All-atom Clashscore : 6.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.70 % Favored : 97.30 % Rotamer: Outliers : 0.11 % Allowed : 1.66 % Favored : 98.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.73 (0.25), residues: 1074 helix: 1.57 (0.23), residues: 464 sheet: 1.08 (0.38), residues: 166 loop : -0.93 (0.29), residues: 444 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP H 702 HIS 0.004 0.001 HIS H 159 PHE 0.013 0.002 PHE F 108 TYR 0.012 0.002 TYR H 669 ARG 0.003 0.000 ARG G 44 Details of bonding type rmsd hydrogen bonds : bond 0.12728 ( 608) hydrogen bonds : angle 6.47464 ( 1605) covalent geometry : bond 0.00530 (12880) covalent geometry : angle 0.64520 (18164) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2148 Ramachandran restraints generated. 1074 Oldfield, 0 Emsley, 1074 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2148 Ramachandran restraints generated. 1074 Oldfield, 0 Emsley, 1074 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 254 residues out of total 928 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 253 time to evaluate : 1.043 Fit side-chains REVERT: C 11 TYR cc_start: 0.8973 (t80) cc_final: 0.8465 (t80) REVERT: C 24 LYS cc_start: 0.9110 (ttmm) cc_final: 0.8878 (ttmp) REVERT: C 40 ASN cc_start: 0.8612 (m-40) cc_final: 0.8408 (m-40) REVERT: C 42 GLU cc_start: 0.8368 (tt0) cc_final: 0.7908 (mt-10) REVERT: C 93 ASN cc_start: 0.8012 (m-40) cc_final: 0.7210 (p0) REVERT: E 1 MET cc_start: 0.6187 (mtm) cc_final: 0.5325 (mmp) REVERT: E 3 ARG cc_start: 0.7643 (tpt170) cc_final: 0.6785 (ttp80) REVERT: H 29 MET cc_start: 0.4956 (ptp) cc_final: 0.4246 (tpt) REVERT: H 198 ARG cc_start: 0.7365 (ttp-170) cc_final: 0.7051 (mtp85) REVERT: H 741 SER cc_start: 0.8215 (t) cc_final: 0.7978 (p) outliers start: 1 outliers final: 1 residues processed: 253 average time/residue: 1.5062 time to fit residues: 408.2806 Evaluate side-chains 141 residues out of total 928 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 140 time to evaluate : 1.041 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain F residue 83 ILE Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 124 random chunks: chunk 104 optimal weight: 2.9990 chunk 93 optimal weight: 6.9990 chunk 52 optimal weight: 3.9990 chunk 32 optimal weight: 5.9990 chunk 63 optimal weight: 0.4980 chunk 50 optimal weight: 1.9990 chunk 97 optimal weight: 9.9990 chunk 37 optimal weight: 1.9990 chunk 59 optimal weight: 0.7980 chunk 72 optimal weight: 0.6980 chunk 112 optimal weight: 0.9980 overall best weight: 0.9982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F 60 ASN H 108 GLN H 780 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3980 r_free = 0.3980 target = 0.149870 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 83)----------------| | r_work = 0.3658 r_free = 0.3658 target = 0.121624 restraints weight = 14429.541| |-----------------------------------------------------------------------------| r_work (start): 0.3639 rms_B_bonded: 1.22 r_work: 0.3416 rms_B_bonded: 1.96 restraints_weight: 0.5000 r_work: 0.3303 rms_B_bonded: 3.26 restraints_weight: 0.2500 r_work (final): 0.3303 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8288 moved from start: 0.1948 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.046 12880 Z= 0.212 Angle : 0.618 9.792 18164 Z= 0.357 Chirality : 0.039 0.166 2016 Planarity : 0.005 0.053 1716 Dihedral : 27.441 174.072 3278 Min Nonbonded Distance : 1.941 Molprobity Statistics. All-atom Clashscore : 7.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.98 % Favored : 97.02 % Rotamer: Outliers : 4.53 % Allowed : 13.69 % Favored : 81.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.04 (0.26), residues: 1074 helix: 2.10 (0.23), residues: 458 sheet: 0.67 (0.36), residues: 196 loop : -0.90 (0.30), residues: 420 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP H 33 HIS 0.009 0.001 HIS H 780 PHE 0.022 0.002 PHE H 16 TYR 0.014 0.001 TYR F 52 ARG 0.006 0.000 ARG H 566 Details of bonding type rmsd hydrogen bonds : bond 0.04403 ( 608) hydrogen bonds : angle 4.72318 ( 1605) covalent geometry : bond 0.00469 (12880) covalent geometry : angle 0.61841 (18164) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2148 Ramachandran restraints generated. 1074 Oldfield, 0 Emsley, 1074 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2148 Ramachandran restraints generated. 1074 Oldfield, 0 Emsley, 1074 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 199 residues out of total 928 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 158 time to evaluate : 1.099 Fit side-chains REVERT: C 93 ASN cc_start: 0.7855 (m-40) cc_final: 0.7232 (p0) REVERT: D 69 LYS cc_start: 0.7316 (OUTLIER) cc_final: 0.7037 (mptt) REVERT: E 1 MET cc_start: 0.6440 (mtm) cc_final: 0.6093 (mmp) REVERT: F 40 GLU cc_start: 0.8060 (OUTLIER) cc_final: 0.7038 (tm-30) REVERT: F 72 MET cc_start: 0.8476 (ttm) cc_final: 0.7951 (mtp) REVERT: G 14 VAL cc_start: 0.6999 (t) cc_final: 0.6650 (m) REVERT: G 73 ARG cc_start: 0.7483 (mtt90) cc_final: 0.7056 (mtm180) REVERT: H 29 MET cc_start: 0.4886 (ptp) cc_final: 0.4219 (tpt) REVERT: H 182 LYS cc_start: 0.8664 (OUTLIER) cc_final: 0.8086 (mppt) REVERT: H 198 ARG cc_start: 0.7352 (ttp-170) cc_final: 0.7125 (mtm110) outliers start: 41 outliers final: 16 residues processed: 180 average time/residue: 1.4763 time to fit residues: 285.7185 Evaluate side-chains 154 residues out of total 928 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 135 time to evaluate : 1.022 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 15 LYS Chi-restraints excluded: chain D residue 69 LYS Chi-restraints excluded: chain E residue 6 THR Chi-restraints excluded: chain E residue 66 LEU Chi-restraints excluded: chain F residue 40 GLU Chi-restraints excluded: chain F residue 83 ILE Chi-restraints excluded: chain F residue 114 SER Chi-restraints excluded: chain F residue 115 GLU Chi-restraints excluded: chain G residue 71 THR Chi-restraints excluded: chain H residue 12 SER Chi-restraints excluded: chain H residue 85 SER Chi-restraints excluded: chain H residue 90 VAL Chi-restraints excluded: chain H residue 110 VAL Chi-restraints excluded: chain H residue 148 THR Chi-restraints excluded: chain H residue 182 LYS Chi-restraints excluded: chain H residue 278 MET Chi-restraints excluded: chain H residue 629 VAL Chi-restraints excluded: chain H residue 787 THR Chi-restraints excluded: chain H residue 791 SER Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 124 random chunks: chunk 50 optimal weight: 1.9990 chunk 12 optimal weight: 1.9990 chunk 96 optimal weight: 0.7980 chunk 110 optimal weight: 1.9990 chunk 40 optimal weight: 2.9990 chunk 103 optimal weight: 0.6980 chunk 35 optimal weight: 0.5980 chunk 112 optimal weight: 0.8980 chunk 85 optimal weight: 0.0270 chunk 106 optimal weight: 0.9980 chunk 2 optimal weight: 1.9990 overall best weight: 0.6038 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 780 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3994 r_free = 0.3994 target = 0.150899 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 110)---------------| | r_work = 0.3678 r_free = 0.3678 target = 0.122451 restraints weight = 14454.096| |-----------------------------------------------------------------------------| r_work (start): 0.3650 rms_B_bonded: 1.21 r_work: 0.3431 rms_B_bonded: 1.94 restraints_weight: 0.5000 r_work: 0.3316 rms_B_bonded: 3.22 restraints_weight: 0.2500 r_work (final): 0.3316 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8263 moved from start: 0.2325 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 12880 Z= 0.165 Angle : 0.578 10.267 18164 Z= 0.333 Chirality : 0.036 0.161 2016 Planarity : 0.004 0.052 1716 Dihedral : 27.359 175.468 3278 Min Nonbonded Distance : 1.977 Molprobity Statistics. All-atom Clashscore : 7.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.70 % Favored : 97.30 % Rotamer: Outliers : 4.30 % Allowed : 16.67 % Favored : 79.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.18 (0.26), residues: 1074 helix: 2.21 (0.23), residues: 462 sheet: 0.85 (0.38), residues: 190 loop : -0.89 (0.30), residues: 422 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP H 33 HIS 0.008 0.001 HIS H 780 PHE 0.024 0.001 PHE H 16 TYR 0.014 0.001 TYR F 52 ARG 0.004 0.000 ARG H 822 Details of bonding type rmsd hydrogen bonds : bond 0.03840 ( 608) hydrogen bonds : angle 4.36791 ( 1605) covalent geometry : bond 0.00358 (12880) covalent geometry : angle 0.57840 (18164) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2148 Ramachandran restraints generated. 1074 Oldfield, 0 Emsley, 1074 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2148 Ramachandran restraints generated. 1074 Oldfield, 0 Emsley, 1074 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 182 residues out of total 928 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 143 time to evaluate : 1.397 Fit side-chains REVERT: C 15 LYS cc_start: 0.8720 (OUTLIER) cc_final: 0.8484 (mtpm) REVERT: C 42 GLU cc_start: 0.7960 (tt0) cc_final: 0.7717 (mt-10) REVERT: E 1 MET cc_start: 0.6388 (mtm) cc_final: 0.6044 (mmp) REVERT: F 72 MET cc_start: 0.8301 (ttm) cc_final: 0.8081 (mtp) REVERT: G 14 VAL cc_start: 0.7038 (t) cc_final: 0.6787 (m) REVERT: G 35 ARG cc_start: 0.8002 (OUTLIER) cc_final: 0.7701 (ptt180) REVERT: G 73 ARG cc_start: 0.7412 (mtt90) cc_final: 0.7065 (mtm180) REVERT: H 198 ARG cc_start: 0.7385 (ttp-170) cc_final: 0.6965 (ptm160) REVERT: H 709 LYS cc_start: 0.8727 (mppt) cc_final: 0.8497 (mttt) outliers start: 39 outliers final: 16 residues processed: 167 average time/residue: 1.7946 time to fit residues: 324.4622 Evaluate side-chains 147 residues out of total 928 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 129 time to evaluate : 1.354 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 15 LYS Chi-restraints excluded: chain C residue 91 VAL Chi-restraints excluded: chain E residue 6 THR Chi-restraints excluded: chain E residue 66 LEU Chi-restraints excluded: chain F residue 43 ILE Chi-restraints excluded: chain F residue 77 GLU Chi-restraints excluded: chain G residue 35 ARG Chi-restraints excluded: chain G residue 71 THR Chi-restraints excluded: chain H residue 48 ASP Chi-restraints excluded: chain H residue 85 SER Chi-restraints excluded: chain H residue 90 VAL Chi-restraints excluded: chain H residue 92 MET Chi-restraints excluded: chain H residue 148 THR Chi-restraints excluded: chain H residue 216 GLU Chi-restraints excluded: chain H residue 629 VAL Chi-restraints excluded: chain H residue 689 GLU Chi-restraints excluded: chain H residue 787 THR Chi-restraints excluded: chain H residue 823 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 124 random chunks: chunk 35 optimal weight: 1.9990 chunk 123 optimal weight: 0.9980 chunk 119 optimal weight: 1.9990 chunk 38 optimal weight: 1.9990 chunk 31 optimal weight: 3.9990 chunk 66 optimal weight: 7.9990 chunk 36 optimal weight: 1.9990 chunk 47 optimal weight: 1.9990 chunk 14 optimal weight: 0.9980 chunk 19 optimal weight: 1.9990 chunk 30 optimal weight: 0.5980 overall best weight: 1.3184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 780 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3954 r_free = 0.3954 target = 0.147563 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 59)----------------| | r_work = 0.3761 r_free = 0.3761 target = 0.127562 restraints weight = 14493.963| |-----------------------------------------------------------------------------| r_work (start): 0.3744 rms_B_bonded: 0.79 r_work: 0.3424 rms_B_bonded: 1.66 restraints_weight: 0.5000 r_work: 0.3315 rms_B_bonded: 2.80 restraints_weight: 0.2500 r_work (final): 0.3315 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8273 moved from start: 0.2675 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.049 12880 Z= 0.250 Angle : 0.639 11.192 18164 Z= 0.365 Chirality : 0.040 0.179 2016 Planarity : 0.005 0.053 1716 Dihedral : 27.592 177.396 3276 Min Nonbonded Distance : 1.915 Molprobity Statistics. All-atom Clashscore : 7.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.82 % Favored : 96.18 % Rotamer: Outliers : 4.86 % Allowed : 16.67 % Favored : 78.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.95 (0.26), residues: 1074 helix: 2.06 (0.23), residues: 461 sheet: 0.56 (0.36), residues: 210 loop : -1.05 (0.30), residues: 403 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP H 33 HIS 0.009 0.001 HIS H 780 PHE 0.022 0.002 PHE H 16 TYR 0.014 0.002 TYR G 52 ARG 0.005 0.001 ARG C 77 Details of bonding type rmsd hydrogen bonds : bond 0.04705 ( 608) hydrogen bonds : angle 4.49589 ( 1605) covalent geometry : bond 0.00555 (12880) covalent geometry : angle 0.63911 (18164) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2148 Ramachandran restraints generated. 1074 Oldfield, 0 Emsley, 1074 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2148 Ramachandran restraints generated. 1074 Oldfield, 0 Emsley, 1074 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 184 residues out of total 928 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 140 time to evaluate : 1.828 Fit side-chains REVERT: E 1 MET cc_start: 0.6218 (mtm) cc_final: 0.5947 (mmp) REVERT: E 106 ILE cc_start: 0.8866 (OUTLIER) cc_final: 0.8483 (mp) REVERT: G 14 VAL cc_start: 0.7108 (t) cc_final: 0.6842 (m) REVERT: G 73 ARG cc_start: 0.7518 (mtt90) cc_final: 0.7144 (mtm180) REVERT: H 75 ARG cc_start: 0.8315 (OUTLIER) cc_final: 0.7672 (mmm160) REVERT: H 252 LYS cc_start: 0.7626 (OUTLIER) cc_final: 0.7137 (mmtp) REVERT: H 263 LYS cc_start: 0.6260 (OUTLIER) cc_final: 0.5951 (mtmt) REVERT: H 709 LYS cc_start: 0.8777 (mppt) cc_final: 0.8535 (mttt) outliers start: 44 outliers final: 22 residues processed: 166 average time/residue: 1.6806 time to fit residues: 300.0559 Evaluate side-chains 154 residues out of total 928 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 128 time to evaluate : 1.551 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 15 LYS Chi-restraints excluded: chain C residue 91 VAL Chi-restraints excluded: chain D residue 20 LYS Chi-restraints excluded: chain D residue 70 VAL Chi-restraints excluded: chain E residue 6 THR Chi-restraints excluded: chain E residue 66 LEU Chi-restraints excluded: chain E residue 106 ILE Chi-restraints excluded: chain F residue 43 ILE Chi-restraints excluded: chain F residue 77 GLU Chi-restraints excluded: chain F residue 114 SER Chi-restraints excluded: chain G residue 22 VAL Chi-restraints excluded: chain G residue 26 LEU Chi-restraints excluded: chain G residue 71 THR Chi-restraints excluded: chain H residue 48 ASP Chi-restraints excluded: chain H residue 75 ARG Chi-restraints excluded: chain H residue 85 SER Chi-restraints excluded: chain H residue 90 VAL Chi-restraints excluded: chain H residue 110 VAL Chi-restraints excluded: chain H residue 148 THR Chi-restraints excluded: chain H residue 216 GLU Chi-restraints excluded: chain H residue 252 LYS Chi-restraints excluded: chain H residue 263 LYS Chi-restraints excluded: chain H residue 278 MET Chi-restraints excluded: chain H residue 629 VAL Chi-restraints excluded: chain H residue 689 GLU Chi-restraints excluded: chain H residue 787 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 124 random chunks: chunk 89 optimal weight: 3.9990 chunk 84 optimal weight: 1.9990 chunk 114 optimal weight: 0.4980 chunk 111 optimal weight: 1.9990 chunk 37 optimal weight: 0.9980 chunk 100 optimal weight: 1.9990 chunk 98 optimal weight: 5.9990 chunk 14 optimal weight: 0.9990 chunk 116 optimal weight: 0.4980 chunk 113 optimal weight: 1.9990 chunk 13 optimal weight: 1.9990 overall best weight: 0.9984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F 87 ASN H 780 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3963 r_free = 0.3963 target = 0.148424 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3769 r_free = 0.3769 target = 0.128129 restraints weight = 14439.608| |-----------------------------------------------------------------------------| r_work (start): 0.3752 rms_B_bonded: 0.71 r_work: 0.3449 rms_B_bonded: 1.53 restraints_weight: 0.5000 r_work: 0.3343 rms_B_bonded: 2.56 restraints_weight: 0.2500 r_work (final): 0.3343 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8230 moved from start: 0.2836 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.047 12880 Z= 0.210 Angle : 0.615 11.456 18164 Z= 0.351 Chirality : 0.038 0.159 2016 Planarity : 0.005 0.051 1716 Dihedral : 27.509 176.053 3276 Min Nonbonded Distance : 1.934 Molprobity Statistics. All-atom Clashscore : 7.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.17 % Favored : 96.83 % Rotamer: Outliers : 4.86 % Allowed : 17.77 % Favored : 77.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.92 (0.26), residues: 1074 helix: 2.09 (0.23), residues: 461 sheet: 0.48 (0.36), residues: 208 loop : -1.08 (0.30), residues: 405 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP H 33 HIS 0.010 0.001 HIS H 780 PHE 0.027 0.002 PHE H 16 TYR 0.021 0.002 TYR G 52 ARG 0.004 0.000 ARG C 77 Details of bonding type rmsd hydrogen bonds : bond 0.04137 ( 608) hydrogen bonds : angle 4.37452 ( 1605) covalent geometry : bond 0.00464 (12880) covalent geometry : angle 0.61451 (18164) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2148 Ramachandran restraints generated. 1074 Oldfield, 0 Emsley, 1074 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2148 Ramachandran restraints generated. 1074 Oldfield, 0 Emsley, 1074 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 177 residues out of total 928 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 133 time to evaluate : 1.003 Fit side-chains REVERT: C 36 ARG cc_start: 0.8162 (mtt90) cc_final: 0.7870 (mmt90) REVERT: C 42 GLU cc_start: 0.7952 (tt0) cc_final: 0.7721 (mt-10) REVERT: E 1 MET cc_start: 0.6167 (mtm) cc_final: 0.5872 (mmp) REVERT: E 106 ILE cc_start: 0.8865 (OUTLIER) cc_final: 0.8493 (mp) REVERT: G 14 VAL cc_start: 0.7048 (t) cc_final: 0.6789 (m) REVERT: G 73 ARG cc_start: 0.7508 (mtt90) cc_final: 0.7184 (mtm180) REVERT: H 75 ARG cc_start: 0.8263 (OUTLIER) cc_final: 0.7647 (mmm160) REVERT: H 709 LYS cc_start: 0.8767 (mppt) cc_final: 0.8519 (mttt) outliers start: 44 outliers final: 24 residues processed: 162 average time/residue: 1.3606 time to fit residues: 237.7375 Evaluate side-chains 155 residues out of total 928 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 129 time to evaluate : 1.094 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 91 VAL Chi-restraints excluded: chain D residue 20 LYS Chi-restraints excluded: chain E residue 6 THR Chi-restraints excluded: chain E residue 66 LEU Chi-restraints excluded: chain E residue 86 LYS Chi-restraints excluded: chain E residue 106 ILE Chi-restraints excluded: chain F residue 17 LYS Chi-restraints excluded: chain F residue 43 ILE Chi-restraints excluded: chain F residue 77 GLU Chi-restraints excluded: chain F residue 114 SER Chi-restraints excluded: chain G residue 22 VAL Chi-restraints excluded: chain G residue 26 LEU Chi-restraints excluded: chain G residue 71 THR Chi-restraints excluded: chain H residue 48 ASP Chi-restraints excluded: chain H residue 49 LYS Chi-restraints excluded: chain H residue 75 ARG Chi-restraints excluded: chain H residue 85 SER Chi-restraints excluded: chain H residue 90 VAL Chi-restraints excluded: chain H residue 110 VAL Chi-restraints excluded: chain H residue 148 THR Chi-restraints excluded: chain H residue 216 GLU Chi-restraints excluded: chain H residue 268 VAL Chi-restraints excluded: chain H residue 629 VAL Chi-restraints excluded: chain H residue 689 GLU Chi-restraints excluded: chain H residue 780 HIS Chi-restraints excluded: chain H residue 787 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 124 random chunks: chunk 61 optimal weight: 0.7980 chunk 89 optimal weight: 1.9990 chunk 26 optimal weight: 0.9980 chunk 48 optimal weight: 1.9990 chunk 43 optimal weight: 1.9990 chunk 76 optimal weight: 0.5980 chunk 9 optimal weight: 2.9990 chunk 16 optimal weight: 3.9990 chunk 47 optimal weight: 1.9990 chunk 69 optimal weight: 3.9990 chunk 19 optimal weight: 0.9990 overall best weight: 1.0784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F 87 ASN H 660 ASN H 780 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3956 r_free = 0.3956 target = 0.147861 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 73)----------------| | r_work = 0.3646 r_free = 0.3646 target = 0.120658 restraints weight = 14678.990| |-----------------------------------------------------------------------------| r_work (start): 0.3625 rms_B_bonded: 1.32 r_work: 0.3392 rms_B_bonded: 1.96 restraints_weight: 0.5000 r_work: 0.3278 rms_B_bonded: 3.28 restraints_weight: 0.2500 r_work (final): 0.3278 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8315 moved from start: 0.2945 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.047 12880 Z= 0.219 Angle : 0.622 11.101 18164 Z= 0.354 Chirality : 0.038 0.179 2016 Planarity : 0.005 0.051 1716 Dihedral : 27.515 176.290 3276 Min Nonbonded Distance : 1.925 Molprobity Statistics. All-atom Clashscore : 7.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.72 % Favored : 96.28 % Rotamer: Outliers : 5.30 % Allowed : 17.66 % Favored : 77.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.86 (0.25), residues: 1074 helix: 2.06 (0.23), residues: 461 sheet: 0.42 (0.36), residues: 208 loop : -1.14 (0.30), residues: 405 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP H 33 HIS 0.018 0.001 HIS H 780 PHE 0.024 0.002 PHE H 16 TYR 0.012 0.001 TYR C 11 ARG 0.004 0.000 ARG H 262 Details of bonding type rmsd hydrogen bonds : bond 0.04250 ( 608) hydrogen bonds : angle 4.38749 ( 1605) covalent geometry : bond 0.00487 (12880) covalent geometry : angle 0.62245 (18164) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2148 Ramachandran restraints generated. 1074 Oldfield, 0 Emsley, 1074 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2148 Ramachandran restraints generated. 1074 Oldfield, 0 Emsley, 1074 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 186 residues out of total 928 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 138 time to evaluate : 1.025 Fit side-chains REVERT: C 42 GLU cc_start: 0.8010 (tt0) cc_final: 0.7769 (mt-10) REVERT: E 1 MET cc_start: 0.6323 (mtm) cc_final: 0.5995 (mmp) REVERT: E 106 ILE cc_start: 0.8880 (OUTLIER) cc_final: 0.8465 (mp) REVERT: F 40 GLU cc_start: 0.8085 (OUTLIER) cc_final: 0.6913 (tm-30) REVERT: G 14 VAL cc_start: 0.7120 (t) cc_final: 0.6794 (m) REVERT: H 75 ARG cc_start: 0.8289 (OUTLIER) cc_final: 0.7708 (mmm160) REVERT: H 152 GLN cc_start: 0.7701 (mm-40) cc_final: 0.7161 (mm-40) REVERT: H 252 LYS cc_start: 0.7607 (OUTLIER) cc_final: 0.7120 (mmtp) REVERT: H 263 LYS cc_start: 0.6491 (OUTLIER) cc_final: 0.5839 (mtmt) outliers start: 48 outliers final: 24 residues processed: 167 average time/residue: 1.4208 time to fit residues: 257.2859 Evaluate side-chains 159 residues out of total 928 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 130 time to evaluate : 1.117 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 15 LYS Chi-restraints excluded: chain C residue 91 VAL Chi-restraints excluded: chain D residue 20 LYS Chi-restraints excluded: chain D residue 70 VAL Chi-restraints excluded: chain E residue 6 THR Chi-restraints excluded: chain E residue 66 LEU Chi-restraints excluded: chain E residue 106 ILE Chi-restraints excluded: chain F residue 17 LYS Chi-restraints excluded: chain F residue 40 GLU Chi-restraints excluded: chain F residue 43 ILE Chi-restraints excluded: chain F residue 77 GLU Chi-restraints excluded: chain F residue 114 SER Chi-restraints excluded: chain G residue 22 VAL Chi-restraints excluded: chain G residue 26 LEU Chi-restraints excluded: chain G residue 71 THR Chi-restraints excluded: chain H residue 48 ASP Chi-restraints excluded: chain H residue 75 ARG Chi-restraints excluded: chain H residue 85 SER Chi-restraints excluded: chain H residue 90 VAL Chi-restraints excluded: chain H residue 110 VAL Chi-restraints excluded: chain H residue 148 THR Chi-restraints excluded: chain H residue 216 GLU Chi-restraints excluded: chain H residue 252 LYS Chi-restraints excluded: chain H residue 263 LYS Chi-restraints excluded: chain H residue 268 VAL Chi-restraints excluded: chain H residue 629 VAL Chi-restraints excluded: chain H residue 689 GLU Chi-restraints excluded: chain H residue 780 HIS Chi-restraints excluded: chain H residue 787 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 124 random chunks: chunk 91 optimal weight: 8.9990 chunk 25 optimal weight: 0.8980 chunk 67 optimal weight: 0.6980 chunk 20 optimal weight: 0.8980 chunk 44 optimal weight: 0.5980 chunk 87 optimal weight: 0.6980 chunk 13 optimal weight: 1.9990 chunk 27 optimal weight: 0.7980 chunk 46 optimal weight: 1.9990 chunk 114 optimal weight: 0.9980 chunk 85 optimal weight: 1.9990 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F 87 ASN H 780 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3974 r_free = 0.3974 target = 0.148914 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3788 r_free = 0.3788 target = 0.129572 restraints weight = 14631.585| |-----------------------------------------------------------------------------| r_work (start): 0.3775 rms_B_bonded: 0.72 r_work: 0.3425 rms_B_bonded: 1.88 restraints_weight: 0.5000 r_work: 0.3314 rms_B_bonded: 3.14 restraints_weight: 0.2500 r_work (final): 0.3314 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8267 moved from start: 0.3031 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.046 12880 Z= 0.181 Angle : 0.607 10.737 18164 Z= 0.345 Chirality : 0.037 0.174 2016 Planarity : 0.004 0.050 1716 Dihedral : 27.446 175.169 3276 Min Nonbonded Distance : 1.944 Molprobity Statistics. All-atom Clashscore : 7.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.26 % Favored : 96.74 % Rotamer: Outliers : 4.42 % Allowed : 19.21 % Favored : 76.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.89 (0.25), residues: 1074 helix: 2.12 (0.24), residues: 462 sheet: 0.45 (0.34), residues: 212 loop : -1.20 (0.30), residues: 400 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.002 TRP H 33 HIS 0.016 0.001 HIS H 780 PHE 0.024 0.002 PHE H 16 TYR 0.021 0.001 TYR G 52 ARG 0.009 0.000 ARG G 73 Details of bonding type rmsd hydrogen bonds : bond 0.03887 ( 608) hydrogen bonds : angle 4.30351 ( 1605) covalent geometry : bond 0.00397 (12880) covalent geometry : angle 0.60719 (18164) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2148 Ramachandran restraints generated. 1074 Oldfield, 0 Emsley, 1074 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2148 Ramachandran restraints generated. 1074 Oldfield, 0 Emsley, 1074 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 173 residues out of total 928 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 133 time to evaluate : 1.195 Fit side-chains REVERT: C 36 ARG cc_start: 0.8218 (mtt90) cc_final: 0.7945 (mmt90) REVERT: C 42 GLU cc_start: 0.7975 (tt0) cc_final: 0.7747 (mt-10) REVERT: E 106 ILE cc_start: 0.8830 (OUTLIER) cc_final: 0.8443 (mp) REVERT: G 14 VAL cc_start: 0.7036 (t) cc_final: 0.6790 (m) REVERT: H 31 GLU cc_start: 0.6443 (OUTLIER) cc_final: 0.6157 (tm-30) REVERT: H 152 GLN cc_start: 0.7612 (mm-40) cc_final: 0.7133 (mm-40) REVERT: H 252 LYS cc_start: 0.7551 (OUTLIER) cc_final: 0.7075 (mmtp) REVERT: H 263 LYS cc_start: 0.6453 (OUTLIER) cc_final: 0.5813 (mtmt) outliers start: 40 outliers final: 23 residues processed: 161 average time/residue: 1.6001 time to fit residues: 278.4339 Evaluate side-chains 154 residues out of total 928 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 127 time to evaluate : 2.618 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 91 VAL Chi-restraints excluded: chain D residue 20 LYS Chi-restraints excluded: chain E residue 6 THR Chi-restraints excluded: chain E residue 66 LEU Chi-restraints excluded: chain E residue 106 ILE Chi-restraints excluded: chain F residue 17 LYS Chi-restraints excluded: chain F residue 43 ILE Chi-restraints excluded: chain F residue 77 GLU Chi-restraints excluded: chain F residue 114 SER Chi-restraints excluded: chain G residue 22 VAL Chi-restraints excluded: chain G residue 71 THR Chi-restraints excluded: chain G residue 72 MET Chi-restraints excluded: chain H residue 31 GLU Chi-restraints excluded: chain H residue 48 ASP Chi-restraints excluded: chain H residue 49 LYS Chi-restraints excluded: chain H residue 85 SER Chi-restraints excluded: chain H residue 90 VAL Chi-restraints excluded: chain H residue 110 VAL Chi-restraints excluded: chain H residue 148 THR Chi-restraints excluded: chain H residue 216 GLU Chi-restraints excluded: chain H residue 252 LYS Chi-restraints excluded: chain H residue 263 LYS Chi-restraints excluded: chain H residue 268 VAL Chi-restraints excluded: chain H residue 629 VAL Chi-restraints excluded: chain H residue 689 GLU Chi-restraints excluded: chain H residue 780 HIS Chi-restraints excluded: chain H residue 787 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 124 random chunks: chunk 71 optimal weight: 3.9990 chunk 84 optimal weight: 2.9990 chunk 8 optimal weight: 2.9990 chunk 36 optimal weight: 0.8980 chunk 25 optimal weight: 0.5980 chunk 63 optimal weight: 10.0000 chunk 5 optimal weight: 1.9990 chunk 10 optimal weight: 1.9990 chunk 34 optimal weight: 0.9990 chunk 24 optimal weight: 0.8980 chunk 37 optimal weight: 0.9990 overall best weight: 0.8784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: G 50 HIS H 780 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3969 r_free = 0.3969 target = 0.148454 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 86)----------------| | r_work = 0.3657 r_free = 0.3657 target = 0.121442 restraints weight = 14677.750| |-----------------------------------------------------------------------------| r_work (start): 0.3639 rms_B_bonded: 1.19 r_work: 0.3410 rms_B_bonded: 1.92 restraints_weight: 0.5000 r_work: 0.3297 rms_B_bonded: 3.20 restraints_weight: 0.2500 r_work (final): 0.3297 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8289 moved from start: 0.3101 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.047 12880 Z= 0.196 Angle : 0.630 12.348 18164 Z= 0.351 Chirality : 0.038 0.181 2016 Planarity : 0.004 0.053 1716 Dihedral : 27.440 174.699 3276 Min Nonbonded Distance : 1.931 Molprobity Statistics. All-atom Clashscore : 8.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.45 % Favored : 96.55 % Rotamer: Outliers : 4.75 % Allowed : 19.98 % Favored : 75.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.83 (0.25), residues: 1074 helix: 2.09 (0.23), residues: 462 sheet: 0.41 (0.34), residues: 213 loop : -1.25 (0.29), residues: 399 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP H 33 HIS 0.019 0.001 HIS H 780 PHE 0.028 0.002 PHE H 16 TYR 0.012 0.001 TYR C 11 ARG 0.009 0.000 ARG G 73 Details of bonding type rmsd hydrogen bonds : bond 0.03988 ( 608) hydrogen bonds : angle 4.32061 ( 1605) covalent geometry : bond 0.00434 (12880) covalent geometry : angle 0.62963 (18164) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2148 Ramachandran restraints generated. 1074 Oldfield, 0 Emsley, 1074 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2148 Ramachandran restraints generated. 1074 Oldfield, 0 Emsley, 1074 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 174 residues out of total 928 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 131 time to evaluate : 1.179 Fit side-chains REVERT: C 42 GLU cc_start: 0.7977 (tt0) cc_final: 0.7753 (mt-10) REVERT: E 106 ILE cc_start: 0.8837 (OUTLIER) cc_final: 0.8411 (mp) REVERT: G 14 VAL cc_start: 0.6924 (t) cc_final: 0.6683 (m) REVERT: H 31 GLU cc_start: 0.6443 (OUTLIER) cc_final: 0.6130 (tm-30) REVERT: H 152 GLN cc_start: 0.7588 (mm-40) cc_final: 0.7114 (mm-40) REVERT: H 252 LYS cc_start: 0.7547 (OUTLIER) cc_final: 0.7066 (mmtp) REVERT: H 263 LYS cc_start: 0.6438 (OUTLIER) cc_final: 0.5799 (mtmt) outliers start: 43 outliers final: 26 residues processed: 162 average time/residue: 1.4155 time to fit residues: 248.6481 Evaluate side-chains 158 residues out of total 928 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 128 time to evaluate : 1.068 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 15 LYS Chi-restraints excluded: chain C residue 58 ASN Chi-restraints excluded: chain C residue 91 VAL Chi-restraints excluded: chain D residue 20 LYS Chi-restraints excluded: chain D residue 70 VAL Chi-restraints excluded: chain E residue 6 THR Chi-restraints excluded: chain E residue 66 LEU Chi-restraints excluded: chain E residue 106 ILE Chi-restraints excluded: chain F residue 17 LYS Chi-restraints excluded: chain F residue 43 ILE Chi-restraints excluded: chain F residue 77 GLU Chi-restraints excluded: chain F residue 114 SER Chi-restraints excluded: chain G residue 22 VAL Chi-restraints excluded: chain G residue 26 LEU Chi-restraints excluded: chain G residue 71 THR Chi-restraints excluded: chain H residue 31 GLU Chi-restraints excluded: chain H residue 48 ASP Chi-restraints excluded: chain H residue 49 LYS Chi-restraints excluded: chain H residue 85 SER Chi-restraints excluded: chain H residue 90 VAL Chi-restraints excluded: chain H residue 110 VAL Chi-restraints excluded: chain H residue 148 THR Chi-restraints excluded: chain H residue 216 GLU Chi-restraints excluded: chain H residue 252 LYS Chi-restraints excluded: chain H residue 263 LYS Chi-restraints excluded: chain H residue 268 VAL Chi-restraints excluded: chain H residue 629 VAL Chi-restraints excluded: chain H residue 689 GLU Chi-restraints excluded: chain H residue 780 HIS Chi-restraints excluded: chain H residue 787 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 124 random chunks: chunk 63 optimal weight: 5.9990 chunk 122 optimal weight: 3.9990 chunk 67 optimal weight: 0.8980 chunk 33 optimal weight: 4.9990 chunk 45 optimal weight: 0.9990 chunk 70 optimal weight: 5.9990 chunk 100 optimal weight: 1.9990 chunk 42 optimal weight: 1.9990 chunk 47 optimal weight: 0.8980 chunk 16 optimal weight: 2.9990 chunk 22 optimal weight: 0.8980 overall best weight: 1.1384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 780 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3959 r_free = 0.3959 target = 0.147656 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3781 r_free = 0.3781 target = 0.128971 restraints weight = 14616.737| |-----------------------------------------------------------------------------| r_work (start): 0.3769 rms_B_bonded: 0.72 r_work: 0.3396 rms_B_bonded: 2.05 restraints_weight: 0.5000 r_work: 0.3273 rms_B_bonded: 3.51 restraints_weight: 0.2500 r_work (final): 0.3273 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8325 moved from start: 0.3152 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.048 12880 Z= 0.228 Angle : 0.656 14.125 18164 Z= 0.364 Chirality : 0.039 0.196 2016 Planarity : 0.005 0.053 1716 Dihedral : 27.494 173.890 3276 Min Nonbonded Distance : 1.914 Molprobity Statistics. All-atom Clashscore : 7.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.91 % Favored : 96.09 % Rotamer: Outliers : 4.19 % Allowed : 20.64 % Favored : 75.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.74 (0.25), residues: 1074 helix: 2.02 (0.24), residues: 462 sheet: 0.35 (0.34), residues: 213 loop : -1.31 (0.29), residues: 399 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP H 33 HIS 0.018 0.001 HIS H 780 PHE 0.028 0.002 PHE H 16 TYR 0.022 0.002 TYR G 52 ARG 0.009 0.000 ARG G 73 Details of bonding type rmsd hydrogen bonds : bond 0.04275 ( 608) hydrogen bonds : angle 4.39878 ( 1605) covalent geometry : bond 0.00510 (12880) covalent geometry : angle 0.65643 (18164) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2148 Ramachandran restraints generated. 1074 Oldfield, 0 Emsley, 1074 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2148 Ramachandran restraints generated. 1074 Oldfield, 0 Emsley, 1074 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 163 residues out of total 928 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 125 time to evaluate : 1.093 Fit side-chains REVERT: C 42 GLU cc_start: 0.8027 (tt0) cc_final: 0.7778 (mt-10) REVERT: E 106 ILE cc_start: 0.8860 (OUTLIER) cc_final: 0.8436 (mp) REVERT: G 14 VAL cc_start: 0.6922 (t) cc_final: 0.6653 (m) REVERT: H 31 GLU cc_start: 0.6493 (OUTLIER) cc_final: 0.6165 (tt0) REVERT: H 152 GLN cc_start: 0.7633 (mm-40) cc_final: 0.7145 (mm-40) REVERT: H 252 LYS cc_start: 0.7618 (OUTLIER) cc_final: 0.7119 (mmtp) REVERT: H 263 LYS cc_start: 0.6435 (OUTLIER) cc_final: 0.5842 (mtmt) outliers start: 38 outliers final: 27 residues processed: 153 average time/residue: 1.3658 time to fit residues: 226.0463 Evaluate side-chains 155 residues out of total 928 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 124 time to evaluate : 1.095 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 15 LYS Chi-restraints excluded: chain C residue 58 ASN Chi-restraints excluded: chain C residue 91 VAL Chi-restraints excluded: chain D residue 20 LYS Chi-restraints excluded: chain D residue 70 VAL Chi-restraints excluded: chain E residue 6 THR Chi-restraints excluded: chain E residue 66 LEU Chi-restraints excluded: chain E residue 86 LYS Chi-restraints excluded: chain E residue 106 ILE Chi-restraints excluded: chain F residue 17 LYS Chi-restraints excluded: chain F residue 43 ILE Chi-restraints excluded: chain F residue 77 GLU Chi-restraints excluded: chain F residue 114 SER Chi-restraints excluded: chain G residue 22 VAL Chi-restraints excluded: chain G residue 26 LEU Chi-restraints excluded: chain G residue 71 THR Chi-restraints excluded: chain G residue 72 MET Chi-restraints excluded: chain H residue 31 GLU Chi-restraints excluded: chain H residue 48 ASP Chi-restraints excluded: chain H residue 49 LYS Chi-restraints excluded: chain H residue 85 SER Chi-restraints excluded: chain H residue 90 VAL Chi-restraints excluded: chain H residue 110 VAL Chi-restraints excluded: chain H residue 148 THR Chi-restraints excluded: chain H residue 216 GLU Chi-restraints excluded: chain H residue 252 LYS Chi-restraints excluded: chain H residue 263 LYS Chi-restraints excluded: chain H residue 268 VAL Chi-restraints excluded: chain H residue 629 VAL Chi-restraints excluded: chain H residue 689 GLU Chi-restraints excluded: chain H residue 787 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 124 random chunks: chunk 3 optimal weight: 1.9990 chunk 77 optimal weight: 2.9990 chunk 74 optimal weight: 0.6980 chunk 13 optimal weight: 1.9990 chunk 58 optimal weight: 4.9990 chunk 66 optimal weight: 0.9980 chunk 70 optimal weight: 3.9990 chunk 91 optimal weight: 1.9990 chunk 35 optimal weight: 0.5980 chunk 107 optimal weight: 2.9990 chunk 81 optimal weight: 1.9990 overall best weight: 1.2584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F 50 HIS H 780 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3950 r_free = 0.3950 target = 0.146990 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 75)----------------| | r_work = 0.3633 r_free = 0.3633 target = 0.119989 restraints weight = 14587.970| |-----------------------------------------------------------------------------| r_work (start): 0.3613 rms_B_bonded: 1.19 r_work: 0.3379 rms_B_bonded: 1.94 restraints_weight: 0.5000 r_work: 0.3268 rms_B_bonded: 3.21 restraints_weight: 0.2500 r_work (final): 0.3268 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8316 moved from start: 0.3246 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.049 12880 Z= 0.244 Angle : 0.673 14.155 18164 Z= 0.373 Chirality : 0.040 0.195 2016 Planarity : 0.005 0.054 1716 Dihedral : 27.637 173.773 3276 Min Nonbonded Distance : 1.900 Molprobity Statistics. All-atom Clashscore : 7.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.91 % Favored : 96.09 % Rotamer: Outliers : 3.86 % Allowed : 20.86 % Favored : 75.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.68 (0.25), residues: 1074 helix: 1.94 (0.23), residues: 461 sheet: 0.32 (0.34), residues: 213 loop : -1.28 (0.29), residues: 400 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP H 33 HIS 0.012 0.001 HIS H 780 PHE 0.031 0.002 PHE H 16 TYR 0.014 0.002 TYR C 11 ARG 0.009 0.000 ARG G 73 Details of bonding type rmsd hydrogen bonds : bond 0.04479 ( 608) hydrogen bonds : angle 4.47538 ( 1605) covalent geometry : bond 0.00545 (12880) covalent geometry : angle 0.67328 (18164) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2148 Ramachandran restraints generated. 1074 Oldfield, 0 Emsley, 1074 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2148 Ramachandran restraints generated. 1074 Oldfield, 0 Emsley, 1074 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 160 residues out of total 928 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 125 time to evaluate : 0.979 Fit side-chains REVERT: E 106 ILE cc_start: 0.8865 (OUTLIER) cc_final: 0.8443 (mp) REVERT: G 14 VAL cc_start: 0.6920 (t) cc_final: 0.6677 (m) REVERT: G 31 ASN cc_start: 0.7929 (t0) cc_final: 0.7276 (m110) REVERT: H 31 GLU cc_start: 0.6460 (OUTLIER) cc_final: 0.6088 (tt0) REVERT: H 152 GLN cc_start: 0.7597 (mm-40) cc_final: 0.7115 (mm-40) REVERT: H 252 LYS cc_start: 0.7637 (OUTLIER) cc_final: 0.7160 (mmtp) REVERT: H 263 LYS cc_start: 0.6438 (OUTLIER) cc_final: 0.5844 (mtmt) outliers start: 35 outliers final: 25 residues processed: 150 average time/residue: 1.3599 time to fit residues: 219.6546 Evaluate side-chains 151 residues out of total 928 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 122 time to evaluate : 1.023 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 15 LYS Chi-restraints excluded: chain C residue 58 ASN Chi-restraints excluded: chain C residue 91 VAL Chi-restraints excluded: chain D residue 20 LYS Chi-restraints excluded: chain D residue 70 VAL Chi-restraints excluded: chain E residue 6 THR Chi-restraints excluded: chain E residue 66 LEU Chi-restraints excluded: chain E residue 86 LYS Chi-restraints excluded: chain E residue 106 ILE Chi-restraints excluded: chain F residue 17 LYS Chi-restraints excluded: chain F residue 43 ILE Chi-restraints excluded: chain F residue 77 GLU Chi-restraints excluded: chain F residue 114 SER Chi-restraints excluded: chain G residue 22 VAL Chi-restraints excluded: chain G residue 71 THR Chi-restraints excluded: chain H residue 31 GLU Chi-restraints excluded: chain H residue 48 ASP Chi-restraints excluded: chain H residue 85 SER Chi-restraints excluded: chain H residue 90 VAL Chi-restraints excluded: chain H residue 110 VAL Chi-restraints excluded: chain H residue 148 THR Chi-restraints excluded: chain H residue 216 GLU Chi-restraints excluded: chain H residue 252 LYS Chi-restraints excluded: chain H residue 263 LYS Chi-restraints excluded: chain H residue 268 VAL Chi-restraints excluded: chain H residue 629 VAL Chi-restraints excluded: chain H residue 689 GLU Chi-restraints excluded: chain H residue 780 HIS Chi-restraints excluded: chain H residue 787 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 124 random chunks: chunk 30 optimal weight: 1.9990 chunk 41 optimal weight: 0.7980 chunk 83 optimal weight: 2.9990 chunk 50 optimal weight: 0.9980 chunk 15 optimal weight: 1.9990 chunk 73 optimal weight: 0.8980 chunk 1 optimal weight: 2.9990 chunk 79 optimal weight: 1.9990 chunk 54 optimal weight: 0.0980 chunk 47 optimal weight: 4.9990 chunk 16 optimal weight: 2.9990 overall best weight: 0.9582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 130 GLN H 780 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3961 r_free = 0.3961 target = 0.147812 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 76)----------------| | r_work = 0.3664 r_free = 0.3664 target = 0.122079 restraints weight = 14565.466| |-----------------------------------------------------------------------------| r_work (start): 0.3656 rms_B_bonded: 1.08 r_work: 0.3404 rms_B_bonded: 1.91 restraints_weight: 0.5000 r_work: 0.3292 rms_B_bonded: 3.18 restraints_weight: 0.2500 r_work (final): 0.3292 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8296 moved from start: 0.3282 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.048 12880 Z= 0.207 Angle : 0.655 14.497 18164 Z= 0.363 Chirality : 0.038 0.181 2016 Planarity : 0.005 0.053 1716 Dihedral : 27.550 173.763 3276 Min Nonbonded Distance : 1.915 Molprobity Statistics. All-atom Clashscore : 7.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.82 % Favored : 96.18 % Rotamer: Outliers : 3.53 % Allowed : 21.63 % Favored : 74.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.68 (0.25), residues: 1074 helix: 1.93 (0.23), residues: 461 sheet: 0.36 (0.34), residues: 213 loop : -1.29 (0.30), residues: 400 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP H 33 HIS 0.009 0.001 HIS H 780 PHE 0.030 0.002 PHE H 16 TYR 0.023 0.002 TYR G 52 ARG 0.010 0.000 ARG G 73 Details of bonding type rmsd hydrogen bonds : bond 0.04120 ( 608) hydrogen bonds : angle 4.40020 ( 1605) covalent geometry : bond 0.00462 (12880) covalent geometry : angle 0.65529 (18164) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 11325.15 seconds wall clock time: 201 minutes 0.58 seconds (12060.58 seconds total)